Despite their intent, a Benevolent Conspiracy can still be antagonists. Well-Intentioned Extremism is a danger for any viewpoint, and there's always the possibility of a Renegade Splinter Faction developing. It's even possible that they just screwed up and designated the protagonists as enemies when they were really on the same side. And regardless of whether they're really the good guys, they probably don't appreciate being revealed and will take steps to prevent it (though the truly good ones will probably just steal the evidence rather than Make It Look Like an Accident).

Examples:

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Anime and Manga

Hypnos in Digimon Tamers. Sure they're monitoring telecommunications of half the planet, but they're trying to counter other electronic espionage and criminal activities. Plus someone has to make sure the public doesn't freak out when digital monsters attack.

The Speedwagon Foundation in JoJo's Bizarre Adventure seems to have influence that goes beyond what's typically legal. Every time the protagonists run into some sort of trouble with the law, they just need to make a single phone call, and everything's fine. As the law and legal system aren't really equipped to prosecute murderers with supernatural power that are Invisible to Normals, this is arguably necessary.

Comic Books

In one two-part Amazing Spider-Man story during Eric Larson's run, Spidey teamed up with The Punisher to find out who was hoarding thousands of tons of cocaine but not selling it. It turned out that an agency in the actual U.S. Government (which one was not revealed) was behind this scheme. Worried that the economy's dependence on the Gold Standard might be a liability if gold were to lose value in a crisis, this agency was actually considering using cocaine as the new standard, reasoning that drugs always had value. While both Spider-Man and the Punisher knew this was a sick and misguided idea, they decided against exposing it; not only would it be hard for a judge to believe "a man in a mask like me and a walkng gun shop like you" as Spidey put it, knowing about such a thing would hurt — if not destroy — what trust remained in America's government. (However, they did destroy the cocaine. Letting the conspiracy continue was not an option.)

Fan Works

In the fanfic Equestria: A History Revealed, amid the insane conspiracy ramblings, the narrator actually uncovers some information hinting at a genuine conspiracy. In chapters 11 and 12, she finds evidence of a secret meeting between Celestia, Luna, and Star Swirl the Bearded — just before Celestia and Luna became alicorns and were crowned Princesses — and all record of what exactly happened at this meeting was erased. The narrator tries to spin this as evidence that Celestia is actually evil, but the documents strongly imply the conspiracy was for the greater good of Equestria, as it prevented the complete collapse of the nation after the defeat of Discord, and restored stability to the nation by creating a central leadership figure for the ponies to believe in.

Film

The Bureau for Paranormal Research and Defense from the Hellboy films (as opposed to the comics, where they worked openly). This is a secret organization that protects the world from supernatural dangers.

Men in Black: A secret agency on Earth, which started as a Government Conspiracy (but avoids them now, because "they ask too many questions"), covertly coordinates with alien governments to control alien immigration to and from Earth, as well as carefully controlling the importation of advanced alien technology.

The Brotherhood of the Cruciform Sword in Indiana Jones and the Last Crusade were/are a group sworn to keep the Holy Grail a secret and away from those who would misuse its gifts. They have little problem with trying to kill those who would seek the Grail, as they are backed by divine will. Nor do they have a problem with dying themselves to keep it secret if they have to. (MAD, of all things, pointed out in their satire how hypocritical it would be of an organization dedicated to protecting the memory of Jesus Christ to resort to methods He would clearly not approve of.) Indy's response that he just wants to find his father to Kazim's question below shows how benevolent they are, giving him info on how to find him.

Kazim(To Indy): Ask yourself, why do you seek the Cup of Christ? Is it for His glory, or for yours?

The series initially presents the eponymous Foundation as being one of these: a hidden organization that, through its machinations, is attempting to steer human society through the dark ages into a new prosperous age. Later on, the Second Foundation is somewhat presented like this.

And, of course, at the end of the series, it's revealed that the robots from tens of thousands of years ago, who had seemingly disappeared from the galaxy, have been benevolently guiding humanity's path the entire time.

Isaac Asimov's short story "The Dead Past". The government is secretly trying to prevent anyone from developing a time viewer device (a device that can show the past). The protagonists disagree and not only develop such a device, but distribute the plans widely. A government agent then explains to them the reason for the ban: such a time viewer could be used to spy on anyone, anywhere in current time. The widespread availability of such viewers means the effective end of personal privacy for the human race.

Of course, Asimov never answers the corollary: the government has controlled the time viewer for decades, and admits to using it to spy on the protagonists. Personal privacy ended long before, it's just that no-one knew it save the government. Also, the government has similar laws against allunregulated scientific research — presumably enforced via chronoscope.

The Dresden Files: The White Council of wizards attempts to be this for humanity, although opinions are strongly divided as to how well it succeeds. In fact, the official party line's denial of the existence of an evil conspiracy in their midst (despite strong evidence) prompts some characters to form a Benevolent Conspiracy of their own, so they can act against the evil one without censure from their higher-ups.

In the Belisarius Series, the good guys who are movers and shakers of the Byzantine Empire begin their plans for dealing with the evil Malwa without telling the Emperor or Empress, the former of which being something of a paranoiac who sees conspiracies against him and doesn't really trust the titular general out of fear Belisarius' Cincinnatus behavior is just an act, and not for real. This is a downplayed version as Empress Theodora later joins them.

Safehold has the Brethren of Saint Zhermeau, with the goal to destroy the corrupt Path of Inspiration Church, and bring back the knowledge of humanity's true history. Also the Circle, which wants to reform the Corrupt Church from within.

The Order of Solomon in L. Jagi Lamplighter's Prospero's Daughter. Utterly ruthless about quenching all knowledge of the existence of magic — so people resort to trying to help themselves instead of groveling before evil beings to obtain power. The Scientific and Industrial Revolutions were possible only with their unflagging efforts.

Victoria has a Monarchist International that secretly works to reinstate the imperial system of absolute monarchy in Germany and Russia, and backs reactionary paleo-conservative groups in the United States. They are still "benevolent" by comparison because, in this near-future dystopia, the current governments in these countries are all incredibly corrupt borderline dictatorships.

In Dance of the Butterfly, the wealthy and powerful Felcraft family fully embraces their self-imposed duty of protecting humankind from a threat it doesn't even know exists. Keeping this threat a secret, as well as thwarting it, is part of the cover-up.

The Warehouse Agents in Warehouse 13 are a secretive millenia-old organization that finds and hides artifacts so they can't harm anyone and so unscrupulous people can't use them.

UFO: The organization known as SHADO (Supreme Headquarters Alien Defense Organization) uses land, sea, and air units to intercept and destroy attacking/invading UFOs. It also acts to keep the alien attacks a secret, sometimes by erasing the memories of people who encounter aliens or UFOs.

30 Rock: The cast and crew of TGS have one to get Liz laid. She thanks them.

The Task Force VALKYRIE from Hunter: The Vigil is a secret branch of the US military, created to fight against supernatural threats and to enforce The Masquerade. Of course, they only appear benevolent from the mortal standpoint, the other critters of New World of Darkness don't appreciate them much.

the d20 Modern setting has a few groups like this dedicated to protecting humanity from Shadows, the most prominent being Department-7, the one the PCs are most likely to belong to. The only known member other than them is a woman named "Ms. Fellows", who always speaks to them as a hologram (of a woman in a business suit and sunglass) at a studio apartment. Exactly where she broadcasts from is unknown, as is much of the details of the organization.

Deus Ex: Morgan Everett tries to portray the Illuminati as this. And they kinda do come across as one when compared to the more immediate and malevolent conspiracy at hand, set in motion by their spin-off organization Majestic-12. In the "Join Illuminati" ending, Morgan and JC are rebuilding the world - however, Morgan reminds JC they have to do it through proxies.

The Keepers from the Thief series. They're more apathetic than benevolent, but they're (in theory) dedicated to preserving Balance of Power. They just decided that not interfering was the best way to do it.

The Star Cabal style themselves in this way, seeking to curb the Jedi and Sith Orders in general and their tendency towards massive, mutually destructive wars in particular. However, over the centuries, it has grown less noble; not only has it Jumped Off The Slippery Slope in a big way, its members have grown less concerned with keeping the peace and more concerned with how their access to massive resources and information on virtually everything in the galaxy can be used to improve their lives and/or bring down their enemies. After bringing down the Star Cabal, the Imperial Agent has the opportunity to use their Black Codex and "disappear" — erasing themselves from all records and becoming untraceable — in order to become a Benevolent Conspiracy of their own within the Sith Empire.

At the end of the Yavin IV arc of Shadow of Revan, there's a more-or-less official Benevolent Conspiracy formed between Satele Shan and Jace and Theron Malcolm, with the Player Character's involvement. They're an actual Republic joint task force investigating the reborn Sith Emperor but their real goal is basically to act under the Supreme Chancellor's nose if need be. The Chancellor isn't all that happy about this, but when the Supreme Commander of the Republic Army, the Grandmaster of the Jedi Order, and one of their most senior spies, who are coincidentally(?) husband, wife, and son, want to go off and conspire together there's not much you can do about it.

The three secret societies that the player can join in The Secret World generally have good intentions. The Templars are very up front about their desire to defend mankind against occult threats. The Illuminati are more self-serving, but there's no way to get ahead and to the top of the pile if the whole planet has been destroyed. The Dragon have a more enigmatic end goal, involving a study of chaos theory and universal mathematical principles, but they still send agents to intervene in occult crises and protect humanity.

The oldest military order in Guild Wars 2, the Order of Whispers, is a covert organisation that manipulates politics to maintain peace within all nations using knowledge and secrets. They feature prominently as one of the organisations the player character can choose to join as well as being responsible for keeping the charr-human peace treaty intact, among many of their activities the player finds out about.

In ''Perimeter, the Exodus faction is an offshoot of the Freemasons who spearheaded the fantastic science seen in the game.

The Family in Resident Evil 6 is an organization dedicated to the preservation of global stability.

Autumn Bay has the Shadowlight League, who are dedicated to the protection and training of wizards and sorcerers and protecting the world from esoteric threats.

El Goonish Shive: The mysterious government agency that Mr. Verres works for that keeps knowledge of magic hidden from the public. Mr. Verres has stated the reason for this is if people knew that magic existed, and that they could learn it themselves, then dangerous people will get magic too; people that you really don't want to give superpowers to. As it turns out, unknown to even the majority who do know of magic, Magic itself wants to keep itself mostly hidden, with only a few people knowing about it. If knowledge of it becomes too widespread, it will alter the rules of how it works, rendering (almost) everybody powerless. This has happened several times in recorded history already.

RWBY: The circle of senior teachers which run the elite combat academies in the world of Remnant have the best of intentions towards the public, concerning themselves as they do with preventing the creatures of Grimm from overrunning the last few bastions of civilisation on the planet. They go out of their way to share their knowledge of Grimm-hunting, encourage younger faculty to go on the occasional bounty-hunting mission to keep crime rates low, encourage teens and twenty-somethings to develop advanced techniques and meet their foreign counterparts, and throw themselves in harm's way to prevent civilian casualties. However, they are also part of a secret organization who suppress the true history of Remnant from the general public. Because Grimm become more dangerous when large numbers of people feel negative emotions (fear, grief, hate, etc), the group quietly deal with threats most of the world doesn't even know exist, in order to keep projecting an image of safety within the Kingdoms; as a result, they actually do make the Grimm less aggressive as a whole. Befitting the trope, they also are opposed by a far more malevolent conspiracy which has its own cabal that works against the protagonists. The fandom refers to the protagonists' organization as the Ozluminati because their leader is named Ozpin.

Western Animation

In Transformers Prime, Team Prime and the US government secretly work together to defend the Earth from Decepticon invasion. The Autobots also share their advanced technology with humanity in exchange for a safe home and logistical support in defending the human race.

In the South Park episode, "Mystery Of The Urinal Deuce, The Government didn't start 9/11, but they created the 9/11 conspiracy movement. They did it because they don't want to appear as a nation weak enough to let such an attack happen, the movement giving them an illusion of power to some.

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